Mohler added that the region had little time to dry out because of the frequent rounds of wet weather.

The wet pattern led to a delay in planting for some, while already planted pumpkins were lost due to flooding.

"Some places had to re-plant three or four times to get established," University of Illinois Professor of Plant Pathology Mohammad Babadoost said.

In addition to the wet conditions, diseases have also contributed to low yields and quality this year.

While Badadoost does not think there will be a shortage or higher prices this year, he suggests buying canned pumpkins as soon as it they come to the store.

How long the canned pumpkins will be available will depend on the market demand.

"Consumers are driven to make purchases (or in some cases deterred) because of a number of reasons including weather. However, not every person shares the same weather experience and so their reaction to weather and their subsequent consumer behavior varies geographically," AccuWeather Business Intelligence Analyst Tim Loftus said.

Processing pumpkins in Illinois are typically planted in late April or early May with harvesting beginning in mid-August.